@jonnings

Associate Professor at University of Oslo. Interested in bioinformatics, 3D Genome, epigenetics, genomics and gene regulation. Postdoc positions available.

 Oslo
mn.uio.no/ibv/english/people/aca/jonaspau/
Joined February 2011
  • Tweets313
  • Following384
  • Followers1.2K
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Struggling with Hi-C data? Meet hictk: a new toolkit revolutionizing working with .hic and .cool files! Seamless interoperability for a range of file formats, and blazing-fast performance, 3D genomics has just gotten a lot easier. Developer: @robomics academic.oup.com/bioinformat…

hictk: blazing fast toolkit to work with .hic and .cool files

AbstractMotivation. Hi-C is gaining prominence as a method for mapping genome organization. With declining sequencing costs and a growing demand for higher

academic.oup.com
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🚨 PhD in Bioinformatics & Gene Regulation 🚨 Join the Bioinformatics in Life Science initiative through a multidisciplinary project to unravel gene regulation from DNA to proteins, co-supervised by @eviledv @jonnings and me @biovitenskap @NCMMnews! jobbnorge.no/en/available-jo…
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Finally biologists can also use numpy (array programming). Handling e.g. DNA and protein sequences with convenience and speed, like physicists and machine learners for decades have worked with numerical data: nature.com/articles/s41592-0… (1/3)

BioNumPy: array programming for biology

Nature Methods - BioNumPy: array programming for biology

nature.com
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Epigenetics, gene transcription and cancer research X afficionados...Don't forget to register and join our exciting "nuclear topology and 3D chromatin architecture in cancer" online symposium taking place on Monday November 11th! Organized by @jane_skok and @LabMelnick #epigenetics #cancer @NYUGSOM_Path
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🎉 Excited to share the peer-reviewed version of our manuscript describing COBIND, a tool for revealing TF co-binding patterns using non-negative matrix factorization. Great work led by @IevaRau @NCMMnews @NordicEMBL @UniOslo_MED @UniOslo academic.oup.com/nar/advance… @NAR_Open
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Our lab (papantonislab.eu) is still looking for a PhD candidate with a strong computational biology background and a keen interest for genome assembly and #3Dgenomics to join our subproject in the exciting EvoREST initiative on genome evolution. @yourUMG @uniGoettingen
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Jonas Paulsen retweeted
NCMBM@NCMBMnews5 Jun 2024
Thanks to @Vesselinka, here is a great picture from @NCMMnews scientific retreat with @emma_haapaniemi presenting her group's research! #WomenDoScience #InclusionMatters
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Jonas Paulsen retweeted
Xavier Tekpli@XahTekK23 Feb 2024
We are hiring an #engineer in the field of #molecular_biology to work with #single_cell_RNA_sequencing and #spatial_transcriptomics in the context of #breast_cancer research. Apply here: finn.no/job/fulltime/ad.html…

Special Engineer in breast cancer, single cell RNA sequencing and spatial transcriptomic · Oslo ·...

Special Engineer in breast cancer, single cell RNA sequencing and spatial

finn.no
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Last couple of days to apply for this postdoc position to generate deep learning models and expand the great JASPAR and UniBind databases @NCMMnews! It's a fantastic project in a very supportive group with outstanding collaborators!
Anthony Mathelier@AMathelier10 Nov 2023
🧬Opening for a postdoc in my group @NCMMnews @UniOslo @UniOslo_MED @unioslo_mn to generate deep learning models to enhance JASPAR @jaspar_db & UniBind, boosting gene regulation research. Project in collaboration with @anshulkundaje, @WyWyWa. Plz share jobbnorge.no/en/available-jo…
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Congratulations to Eivind Hovig! And thanks for great collaboration through more than two decades! You have made invaluable contributions to FUGE, @elixirnorway and Norwegian bioinformatics and cancer research! – at Mons, Norway
ELIXIR Norway@elixirnorway18 Sep 2023
🎉 Happy 70th Birthday to Eivind Hovig! 🎂🥳 Your outstanding contributions to #bioinformatics have paved the way for groundbreaking research in Norway and beyond. 🧬🇳🇴 Your dedication and expertise are invaluable to us, @UniOslo, @UiO_LifeSci & @Oslounivsykehus. 🏆🔬
portrait photo Eivind Hovid

ALT portrait photo Eivind Hovid

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Associate professor of Medicine (Biochemistry) position open at Institute of Basic Medical Sciences, University of Oslo! We are recruiting a new colleague working within the fields of chromatin biology or membrane dynamics! @UniOslo_MED @WAutophagy jobbnorge.no/en/available-jo…
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Jonas Paulsen retweeted
Rein Aasland@rein_oslo13 Jun 2023
Truly amazing to see the @ELIXIREurope crowd gathered for the All Hands Meeting in Dublin taking bioinformatics to new heights!
ELIXIR Europe@ELIXIREurope8 Jun 2023
🎊 2023 ELIXIR All Hands Meeting #ELIXIR23 has come to an end with @NBlomberg’s closing remarks. 👏 Thank you all for joining us in Dublin and we look forward to seeing you again next year in Uppsala, Sweden 🇸🇪 for #ELIXIR24! @sysbioire #ELIXIR_IE @NBISwe #ELIXIR_SE
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We're excited to share our manuscript describing COBIND, a novel tool for the identification of transcription factor co-binding patterns with non-negative matrix factorization biorxiv.org/content/10.1101/… 1/9

Identification of transcription factor co-binding patterns with non-negative matrix factorization

Transcription factor (TF) binding to DNA is critical to transcription regulation. Although the binding properties of numerous individual TFs are well-documented, a more detailed comprehension of how...

biorxiv.org
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MoDLE, modeling of DNA loop extrusion, from @robomics, @jonnings, simulates DNA contact maps quickly, using low memory. It requires a genome region and the barrier positions in the region eg CTCF binding sites. Predicts effects of deletoins on TADS genomebiology.biomedcentral.…
Comparisoin of MicroC data (top) and MoDLE prediction for a region of Chromosome 2

ALT Comparisoin of MicroC data (top) and MoDLE prediction for a region of Chromosome 2

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New publication: "MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions" with Roberto Rossini and Jonas Paulsen @biovitenskap. @jonnings @robomics @GenomeBiology genomebiology.biomedcentral.…

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

Genome Biology - DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts...

link.springer.com
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Great to see the peer-reviewed version of this work now out. Thanks @jonnings @robomics for having us involved! And congrats again 👏 genomebiology.biomedcentral.…

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

Genome Biology - DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts...

link.springer.com
Jonas Paulsen@jonnings19 Apr 2022
New preprint out! biorxiv.org/cgi/content/shor… MoDLE allows simulating HiC-like contacts generated by loop extrusion genome wide in a matter of minutes. Opens up for exploring underlying features of genome structure. Available on the command line. github.com/paulsengroup/modl… @INC_COST
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Haha! Never underestimate a feeling, I guess. Good luck with the replies 😟
Mariike Kuijjer@mkuijjer10 Aug 2022
second time in my career that a reviewer "feels" the mathematics are wrong, but does not demonstrate why 🤷‍♀️
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Jonas Paulsen retweeted
Thomas Fleischer@TF_828 Jul 2022
Happy to publish our latest work as a preprint in bioRxiv. DNA methylation can predict and explain response to chemotherapy and bevacizumab. biorxiv.org/content/10.1101/…

An integrated ‘omics approach highlights the role of epigenetic events to explain and predict...

Here we present an integrated ‘omics approach for DNA methylation profiling using copy number alteration, gene expression and proteomic data to predict response to therapy and to pinpoint response-...

biorxiv.org
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Very happy to see the peer-reviewed version of this work out at epigeneticsandchromatin.biom… We performed expression-methylation quantitative trait loci in 19 cancer types and identified 13 TFs likely driving DNA methylation patterns around their TFBS in at least 2 cancer types 1/6

Pioneer transcription factors are associated with the modulation of DNA methylation patterns across...

Epigenetics & Chromatin - Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked...

link.springer.com
Anthony Mathelier@AMathelier11 May 2021
Our new preprint is out We found that pioneer TFs are associated with the modulation of DNA methylation patterns around their binding sites in cancer and immune cells across cancers Led by @RozaBLemma w/ @TF_82 E Martinsen @Vesselinka @ragnhildes1 @oddsgab biorxiv.org/content/10.1101/…

Pioneer transcription factors are associated with the modulation of DNA methylation patterns across...

Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regula...

biorxiv.org
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Jonas Paulsen retweeted
Roberto Rossini@robomics19 Apr 2022
Happy to share our latest work! A big thanks to @jonnings for his support and supervision. Many thanks also to our collaborators for their invaluable comments and feedback @torognes, @AMathelier and Vipin Kumar.
Jonas Paulsen@jonnings19 Apr 2022
New preprint out! biorxiv.org/cgi/content/shor… MoDLE allows simulating HiC-like contacts generated by loop extrusion genome wide in a matter of minutes. Opens up for exploring underlying features of genome structure. Available on the command line. github.com/paulsengroup/modl… @INC_COST
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